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Homology Modeling pp 1–31Cite as

Classification of Proteins: Available Structural Space for Molecular Modeling

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Part of the book series: Methods in Molecular Biology ((MIMB,volume 857))

Abstract

The wealth of available protein structural data provides unprecedented opportunity to study and better understand the underlying principles of protein folding and protein structure evolution. A key to achieving this lies in the ability to analyse these data and to organize them in a coherent classification scheme. Over the past years several protein classifications have been developed that aim to group proteins based on their structural relationships. Some of these classification schemes explore the concept of structural neighbourhood (structural continuum), whereas other utilize the notion of protein evolution and thus provide a discrete rather than continuum view of protein structure space. This chapter presents a strategy for classification of proteins with known three-dimensional structure. Steps in the classification process along with basic definitions are introduced. Examples illustrating some fundamental concepts of protein folding and evolution with a special focus on the exceptions to them are presented.

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References

  1. Kendrew, J. C., Bodo, G., Dintzis, H. M., Parrish, R. G., Wyckoff, H., and Phillips, D. C. (1958) A three-dimensional model of the myoglobin molecule obtained by x-ray analysis, Nature 181, 662–666.

    PubMed  CAS  Google Scholar 

  2. Berman, H. M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T. N., Weissig, H., Shindyalov, I. N., and Bourne, P. E. (2000) The Protein Data Bank, Nucleic Acids Res 28, 235–242.

    PubMed  CAS  Google Scholar 

  3. Chothia, C. (1984) Principles that determine the structure of proteins, Annu. Rev. Biochem. 53, 537–572.

    PubMed  CAS  Google Scholar 

  4. Chothia, C., Levitt, M., and Richardson, D. (1977) Structure of proteins: packing of alpha-helices and pleated sheets, Proc. Natl. Acad. Sci. USA 74, 4130–4134.

    PubMed  CAS  Google Scholar 

  5. Levitt, M., and Chothia, C. (1976) Structural patterns in globular proteins, Nature 261, 552–558.

    PubMed  CAS  Google Scholar 

  6. Richardson, J. S. (1977) beta-Sheet topology and the relatedness of proteins, Nature 268, 495–500.

    PubMed  CAS  Google Scholar 

  7. Richardson, J. S. (1981) The anatomy and taxonomy of protein structure, Adv. Protein Chem. 34, 167–339.

    PubMed  CAS  Google Scholar 

  8. Holm, L., and Sander, C. (1994) The FSSP database of structurally aligned protein fold families, Nucleic Acids Res 22, 3600–3609.

    PubMed  CAS  Google Scholar 

  9. Ohkawa, H., Ostell, J., and Bryant, S. (1995) MMDB: an ASN.1 specification for macromolecular structure, Proc Int Conf Intell Syst Mol Biol 3, 259–267.

    PubMed  CAS  Google Scholar 

  10. Murzin, A. G., Brenner, S. E., Hubbard, T., and Chothia, C. (1995) SCOP: a structural classification of proteins database for the investigation of sequences and structures, J Mol Biol 247, 536–540.

    PubMed  CAS  Google Scholar 

  11. Orengo, C. A., Pearl, F. M., Bray, J. E., Todd, A. E., Martin, A. C., Lo Conte, L., and Thornton, J. M. (1999) The CATH Database provides insights into protein structure/function relationships, Nucleic Acids Res 27, 275–279.

    PubMed  CAS  Google Scholar 

  12. Orengo, C. A., Michie, A. D., Jones, S., Jones, D. T., Swindells, M. B., and Thornton, J. M. (1997) CATH – a hierarchic classification of protein domain structures, Structure 5, 1093–1108.

    PubMed  CAS  Google Scholar 

  13. Wetlaufer, D. B. (1973) Nucleation, rapid folding, and globular intrachain regions in proteins, Proc Natl Acad Sci USA 70, 697–701.

    PubMed  CAS  Google Scholar 

  14. Rossmann, M. G., Moras, D., and Olsen, K. W. (1974) Chemical and biological evolution of nucleotide-binding protein, Nature 250, 194–199.

    PubMed  CAS  Google Scholar 

  15. Remaut, H., Bompard-Gilles, C., Goffin, C., Frere, J. M., and Van Beeumen, J. (2001) Structure of the Bacillus subtilis D-aminopeptidase DppA reveals a novel self-compartmentalizing protease, Nat Struct Biol 8, 674–678.

    PubMed  CAS  Google Scholar 

  16. Alden, K., Veretnik, S., and Bourne, P. E. (2010) dConsensus: a tool for displaying domain assignments by multiple structure-based algorithms and for construction of a consensus assignment, BMC Bioinformatics 11, 310.

    PubMed  Google Scholar 

  17. Alexandrov, N., and Shindyalov, I. (2003) PDP: protein domain parser, Bioinformatics 19, 429–430.

    PubMed  CAS  Google Scholar 

  18. Holm, L., and Sander, C. (1994) Parser for protein folding units, Proteins 19, 256-268.

    PubMed  CAS  Google Scholar 

  19. Redfern, O. C., Harrison, A., Dallman, T., Pearl, F. M., and Orengo, C. A. (2007) CATHEDRAL: a fast and effective algorithm to predict folds and domain boundaries from multidomain protein structures, PLoS Comput Biol 3, e232.

    PubMed  Google Scholar 

  20. Siddiqui, A. S., and Barton, G. J. (1995) Continuous and discontinuous domains: an algorithm for the automatic generation of reliable protein domain definitions, Protein Sci 4, 872–884.

    PubMed  CAS  Google Scholar 

  21. Sowdhamini, R., and Blundell, T. L. (1995) An automatic method involving cluster analysis of secondary structures for the identification of domains in proteins, Protein Sci 4, 506–520.

    PubMed  CAS  Google Scholar 

  22. Swindells, M. B. (1995) A procedure for detecting structural domains in proteins, Protein Sci 4, 103–112.

    PubMed  CAS  Google Scholar 

  23. Taylor, W. R. (1999) Protein structural domain identification, Protein Eng 12, 203–216.

    PubMed  CAS  Google Scholar 

  24. Veretnik, S., Bourne, P. E., Alexandrov, N. N., and Shindyalov, I. N. (2004) Toward consistent assignment of structural domains in proteins, J Mol Biol 339, 647–678.

    PubMed  CAS  Google Scholar 

  25. Zhou, H., Xue, B., and Zhou, Y. (2007) DDOMAIN: Dividing structures into domains using a normalized domain-domain interaction profile, Protein Sci 16, 947–955.

    PubMed  CAS  Google Scholar 

  26. Sigrist, C. J., Cerutti, L., de Castro, E., Langendijk-Genevaux, P. S., Bulliard, V., Bairoch, A., and Hulo, N. (2010) PROSITE, a protein domain database for functional characterization and annotation, Nucleic Acids Res 38, D161–166.

    PubMed  CAS  Google Scholar 

  27. Levy, E. D., Pereira-Leal, J. B., Chothia, C., and Teichmann, S. A. (2006) 3D complex: a structural classification of protein complexes, PLoS Comput Biol 2, e155.

    PubMed  Google Scholar 

  28. Andreeva, A., Prlic, A., Hubbard, T. J., and Murzin, A. G. (2007) SISYPHUS – structural alignments for proteins with non-trivial relationships, Nucleic Acids Res 35, D253–259.

    PubMed  CAS  Google Scholar 

  29. Hemmingsen, J. M., Gernert, K. M., Richardson, J. S., and Richardson, D. C. (1994) The tyrosine corner: a feature of most Greek key beta-barrel proteins, Protein Sci 3, 1927–1937.

    PubMed  CAS  Google Scholar 

  30. Brennan, R. G., and Matthews, B. W. (1989) The helix-turn-helix DNA binding motif, J Biol Chem 264, 1903–1906.

    PubMed  CAS  Google Scholar 

  31. Doherty, A. J., Serpell, L. C., and Ponting, C. P. (1996) The helix-hairpin-helix DNA-binding motif: a structural basis for non-sequence-specific recognition of DNA, Nucleic Acids Res 24, 2488–2497.

    PubMed  CAS  Google Scholar 

  32. Religa, T. L., Johnson, C. M., Vu, D. M., Brewer, S. H., Dyer, R. B., and Fersht, A. R. (2007) The helix-turn-helix motif as an ultrafast independently folding domain: the pathway of folding of Engrailed homeodomain, Proc Natl Acad Sci USA 104, 9272–9277.

    PubMed  CAS  Google Scholar 

  33. Andreeva, A., and Murzin, A. G. (2006) Evolution of protein fold in the presence of functional constraints, Current Opinion in Structural Biology 16, 399–408.

    CAS  Google Scholar 

  34. Grishin, N. V. (2001) KH domain: one motif, two folds, Nucleic Acids Res 29, 638–643.

    PubMed  CAS  Google Scholar 

  35. Bellamacina, C. R. (1996) The nicotinamide dinucleotide binding motif: a comparison of nucleotide binding proteins, FASEB J 10, 1257–1269.

    PubMed  CAS  Google Scholar 

  36. Rigden, D. J., and Galperin, M. Y. (2004) The DxDxDG motif for calcium binding: multiple structural contexts and implications for evolution, J Mol Biol 343, 971–984.

    PubMed  CAS  Google Scholar 

  37. Saraste, M., Sibbald, P. R., and Wittinghofer, A. (1990) The P-loop – a common motif in ATP- and GTP-binding proteins, Trends Biochem Sci 15, 430–434.

    PubMed  Google Scholar 

  38. Jonassen, I. (1997) Efficient discovery of conserved patterns using a pattern graph, Comput Appl Biosci 13, 509–522.

    PubMed  CAS  Google Scholar 

  39. Jonassen, I., Collins, J. F., and Higgins, D. G. (1995) Finding flexible patterns in unaligned protein sequences, Protein Sci 4, 1587–1595.

    PubMed  CAS  Google Scholar 

  40. Rigoutsos, I., and Floratos, A. (1998) Combinatorial pattern discovery in biological sequences: The TEIRESIAS algorithm, Bioinformatics 14, 55–67.

    PubMed  CAS  Google Scholar 

  41. Ye, K., Kosters, W. A., and Ijzerman, A. P. (2007) An efficient, versatile and scalable pattern growth approach to mine frequent patterns in unaligned protein sequences, Bioinformatics 23, 687–693.

    PubMed  CAS  Google Scholar 

  42. Kleywegt, G. J. (1999) Recognition of spatial motifs in protein structures, J Mol Biol 285, 1887–1897.

    PubMed  CAS  Google Scholar 

  43. Lee, M. C., Scanlon, M. J., Craik, D. J., and Anderson, M. A. (1999) A novel two-chain proteinase inhibitor generated by circularization of a multidomain precursor protein, Nat Struct Biol 6, 526–530.

    PubMed  CAS  Google Scholar 

  44. Neer, E. J., Schmidt, C. J., Nambudripad, R., and Smith, T. F. (1994) The ancient regulatory-protein family of WD-repeat proteins, Nature 371, 297–300.

    PubMed  CAS  Google Scholar 

  45. Murray, K. B., Gorse, D., and Thornton, J. M. (2002) Wavelet transforms for the characterization and detection of repeating motifs, J Mol Biol 316, 341–363.

    PubMed  CAS  Google Scholar 

  46. Heger, A., and Holm, L. (2000) Rapid automatic detection and alignment of repeats in protein sequences, Proteins 41, 224–237.

    PubMed  CAS  Google Scholar 

  47. Andrade, M. A., Ponting, C. P., Gibson, T. J., and Bork, P. (2000) Homology-based method for identification of protein repeats using statistical significance estimates, J Mol Biol 298, 521–537.

    PubMed  CAS  Google Scholar 

  48. Murray, K. B., Taylor, W. R., and Thornton, J. M. (2004) Toward the detection and validation of repeats in protein structure, Proteins 57, 365–380.

    PubMed  CAS  Google Scholar 

  49. Levy, E. D., Boeri Erba, E., Robinson, C. V., and Teichmann, S. A. (2008) Assembly reflects evolution of protein complexes, Nature 453, 1262–1265.

    PubMed  CAS  Google Scholar 

  50. Chothia, C., and Janin, J. (1975) Principles of protein-protein recognition, Nature 256, 705–708.

    PubMed  CAS  Google Scholar 

  51. Jones, S., and Thornton, J. M. (1997) Analysis of protein-protein interaction sites using surface patches, J Mol Biol 272, 121–132.

    PubMed  CAS  Google Scholar 

  52. Levy, E. D. (2007) PiQSi: protein quaternary structure investigation, Structure 15, 1364–1367.

    PubMed  CAS  Google Scholar 

  53. Janin, J., Bahadur, R. P., and Chakrabarti, P. (2008) Protein-protein interaction and quaternary structure, Q Rev Biophys 41, 133–180.

    PubMed  CAS  Google Scholar 

  54. Stetefeld, J., Jenny, M., Schulthess, T., Landwehr, R., Engel, J., and Kammerer, R. A. (2000) Crystal structure of a naturally occurring parallel right-handed coiled coil tetramer, Nat Struct Biol 7, 772–776.

    PubMed  CAS  Google Scholar 

  55. Kuhnel, K., Jarchau, T., Wolf, E., Schlichting, I., Walter, U., Wittinghofer, A., and Strelkov, S. V. (2004) The VASP tetramerization domain is a right-handed coiled coil based on a 15-residue repeat, Proc Natl Acad Sci USA 101, 17027–17032.

    PubMed  Google Scholar 

  56. Cabezon, E., Runswick, M. J., Leslie, A. G., and Walker, J. E. (2001) The structure of bovine IF(1), the regulatory subunit of mitochondrial F-ATPase, EMBO J 20, 6990–6996.

    PubMed  CAS  Google Scholar 

  57. Nooren, I. M., Kaptein, R., Sauer, R. T., and Boelens, R. (1999) The tetramerization domain of the Mnt repressor consists of two right-handed coiled coils, Nat Struct Biol 6, 755–759.

    PubMed  CAS  Google Scholar 

  58. Walshaw, J., and Woolfson, D. N. (2001) Socket: a program for identifying and analysing coiled-coil motifs within protein structures, J Mol Biol 307, 1427–1450.

    PubMed  CAS  Google Scholar 

  59. Strelkov, S. V., and Burkhard, P. (2002) Analysis of alpha-helical coiled coils with the program TWISTER reveals a structural mechanism for stutter compensation, J Struct Biol 137, 54–64.

    PubMed  CAS  Google Scholar 

  60. Orgel, J. P., Irving, T. C., Miller, A., and Wess, T. J. (2006) Microfibrillar structure of type I collagen in situ, Proc Natl Acad Sci USA 103, 9001–9005.

    PubMed  CAS  Google Scholar 

  61. Henderson, R., and Unwin, P. N. (1975) Three-dimensional model of purple membrane obtained by electron microscopy, Nature 257, 28–32.

    PubMed  CAS  Google Scholar 

  62. Walters, R. F., and DeGrado, W. F. (2006) Helix-packing motifs in membrane proteins, Proc Natl Acad Sci USA 103, 13658–13663.

    PubMed  CAS  Google Scholar 

  63. Guan, L., Mirza, O., Verner, G., Iwata, S., and Kaback, H. R. (2007) Structural determination of wild-type lactose permease, Proc Natl Acad Sci USA 104, 15294–15298.

    PubMed  CAS  Google Scholar 

  64. Abramson, J., Smirnova, I., Kasho, V., Verner, G., Kaback, H. R., and Iwata, S. (2003) Structure and mechanism of the lactose permease of Escherichia coli, Science 301, 610–615.

    PubMed  CAS  Google Scholar 

  65. Gupta, S., Bavro, V. N., D’Mello, R., Tucker, S. J., Venien-Bryan, C., and Chance, M. R. (2010) Conformational changes during the gating of a potassium channel revealed by structural mass spectrometry, Structure 18, 839–846.

    PubMed  CAS  Google Scholar 

  66. Toyoshima, C., and Nomura, H. (2002) Structural changes in the calcium pump accompanying the dissociation of calcium, Nature 418, 605-611.

    PubMed  CAS  Google Scholar 

  67. Olesen, C., Sorensen, T. L., Nielsen, R. C., Moller, J. V., and Nissen, P. (2004) Dephosphorylation of the calcium pump coupled to counterion occlusion, Science 306, 2251–2255.

    PubMed  CAS  Google Scholar 

  68. Huang, Y., Lemieux, M. J., Song, J., Auer, M., and Wang, D. N. (2003) Structure and mechanism of the glycerol-3-phosphate transporter from Escherichia coli, Science 301, 616–620.

    PubMed  CAS  Google Scholar 

  69. Oomen, C. J., van Ulsen, P., van Gelder, P., Feijen, M., Tommassen, J., and Gros, P. (2004) Structure of the translocator domain of a bacterial autotransporter, EMBO J 23, 1257–1266.

    PubMed  CAS  Google Scholar 

  70. Locher, K. P., Rees, B., Koebnik, R., Mitschler, A., Moulinier, L., Rosenbusch, J. P., and Moras, D. (1998) Transmembrane signaling across the ligand-gated FhuA receptor: crystal structures of free and ferrichrome-bound states reveal allosteric changes, Cell 95, 771–778.

    PubMed  CAS  Google Scholar 

  71. Dyson, H. J., and Wright, P. E. (2005) Intrinsically unstructured proteins and their functions, Nat Rev Mol Cell Biol 6, 197–208.

    PubMed  CAS  Google Scholar 

  72. Dunker, A. K., Silman, I., Uversky, V. N., and Sussman, J. L. (2008) Function and structure of inherently disordered proteins, Curr Opin Struct Biol 18, 756–764.

    PubMed  CAS  Google Scholar 

  73. Uversky, V. N., and Dunker, A. K. (2010) Understanding protein non-folding, Biochim Biophys Acta 1804, 1231–1264.

    PubMed  CAS  Google Scholar 

  74. Uversky, V. N. (2002) Natively unfolded proteins: a point where biology waits for physics, Protein Sci 11, 739–756.

    PubMed  CAS  Google Scholar 

  75. Tompa, P. (2002) Intrinsically unstructured proteins, Trends Biochem Sci 27, 527–533.

    PubMed  CAS  Google Scholar 

  76. Joerger, A. C., and Fersht, A. R. (2010) The tumor suppressor p53: from structures to drug discovery, Cold Spring Harb Perspect Biol 2, a000919.

    PubMed  Google Scholar 

  77. Rajagopalan, S., Andreeva, A., Rutherford, T. J., and Fersht, A. R. (2010) Mapping the physical and functional interactions between the tumor suppressors p53 and BRCA2, Proc Natl Acad Sci USA 107, 8587–8592.

    PubMed  CAS  Google Scholar 

  78. Rajagopalan, S., Andreeva, A., Teufel, D. P., Freund, S. M., and Fersht, A. R. (2009) Interaction between the transactivation domain of p53 and PC4 exemplifies acidic activation domains as single-stranded DNA mimics, J Biol Chem 284, 21728–21737.

    PubMed  CAS  Google Scholar 

  79. Jonker, H. R., Wechselberger, R. W., Boelens, R., Folkers, G. E., and Kaptein, R. (2005) Structural properties of the promiscuous VP16 activation domain, Biochemistry 44, 827–839.

    PubMed  CAS  Google Scholar 

  80. Uversky, V. N. (2003) A protein-chameleon: conformational plasticity of alpha-synuclein, a disordered protein involved in neurodegenerative disorders, J Biomol Struct Dyn 21, 211–234.

    PubMed  CAS  Google Scholar 

  81. Linding, R., Jensen, L. J., Diella, F., Bork, P., Gibson, T. J., and Russell, R. B. (2003) Protein disorder prediction: implications for structural proteomics, Structure 11, 1453–1459.

    PubMed  CAS  Google Scholar 

  82. Romero, P., Obradovic, Z., Li, X., Garner, E. C., Brown, C. J., and Dunker, A. K. (2001) Sequence complexity of disordered protein, Proteins 42, 38–48.

    PubMed  CAS  Google Scholar 

  83. Ward, J. J., Sodhi, J. S., McGuffin, L. J., Buxton, B. F., and Jones, D. T. (2004) Prediction and functional analysis of native disorder in proteins from the three kingdoms of life, J Mol Biol 337, 635–645.

    PubMed  CAS  Google Scholar 

  84. Sickmeier, M., Hamilton, J. A., LeGall, T., Vacic, V., Cortese, M. S., Tantos, A., Szabo, B., Tompa, P., Chen, J., Uversky, V. N., Obradovic, Z., and Dunker, A. K. (2007) DisProt: the Database of Disordered Proteins, Nucleic Acids Res 35, D786–793.

    PubMed  CAS  Google Scholar 

  85. Altschul, S. F., Madden, T. L., Schaffer, A. A., Zhang, J., Zhang, Z., Miller, W., and Lipman, D. J. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs, Nucleic Acids Res 25, 3389–3402.

    PubMed  CAS  Google Scholar 

  86. Johnson, L. S., Eddy, S. R., and Portugaly, E. (2010) Hidden Markov model speed heuristic and iterative HMM search procedure, BMC Bioinformatics 11, 431.

    PubMed  Google Scholar 

  87. Madera, M. (2008) Profile Comparer: a program for scoring and aligning profile hidden Markov models, Bioinformatics 24, 2630–2631.

    PubMed  CAS  Google Scholar 

  88. Sadreyev, R. I., Tang, M., Kim, B. H., and Grishin, N. V. (2009) COMPASS server for homology detection: improved statistical accuracy, speed and functionality, Nucleic Acids Res 37, W90–94.

    PubMed  CAS  Google Scholar 

  89. Andreeva, A., Prlic, A., Hubbard, T. J., and Murzin, A. G. (2007) SISYPHUS – structural alignments for proteins with non-trivial relationships, Nucleic Acids Res. 35, D253–259.

    PubMed  CAS  Google Scholar 

  90. Grishin, N. V. (2001) Fold change in evolution of protein structures, J Struct Biol 134, 167–185.

    PubMed  CAS  Google Scholar 

  91. Kinch, L. N., and Grishin, N. V. (2002) Evolution of protein structures and functions, Curr Opin Struct Biol 12, 400–408.

    PubMed  CAS  Google Scholar 

  92. Alva, V., Koretke, K. K., Coles, M., and Lupas, A. N. (2008) Cradle-loop barrels and the concept of metafolds in protein classification by natural descent, Curr Opin Struct Biol 18, 358–365.

    PubMed  CAS  Google Scholar 

  93. Anfinsen, C. B. (1973) Principles that govern the folding of protein chains, Science 181, 223–230.

    PubMed  CAS  Google Scholar 

  94. Anfinsen, C. B., Haber, E., Sela, M., and White, F. H., Jr. (1961) The kinetics of formation of native ribonuclease during oxidation of the reduced polypeptide chain, Proc Natl Acad Sci USA 47, 1309–1314.

    PubMed  CAS  Google Scholar 

  95. Luo, X., Tang, Z., Xia, G., Wassmann, K., Matsumoto, T., Rizo, J., and Yu, H. (2004) The Mad2 spindle checkpoint protein has two distinct natively folded states, Nat Struct Mol Biol 11, 338–345.

    PubMed  CAS  Google Scholar 

  96. Tuinstra, R. L., Peterson, F. C., Kutlesa, S., Elgin, E. S., Kron, M. A., and Volkman, B. F. (2008) Interconversion between two unrelated protein folds in the lymphotactin native state, Proc Natl Acad Sci USA 105, 5057–5062.

    PubMed  CAS  Google Scholar 

  97. Cabrita, L. D., and Bottomley, S. P. (2004) How do proteins avoid becoming too stable? Biophysical studies into metastable proteins, Eur Biophys J 33, 83–88.

    PubMed  CAS  Google Scholar 

  98. Bullough, P. A., Hughson, F. M., Skehel, J. J., and Wiley, D. C. (1994) Structure of influenza haemagglutinin at the pH of membrane fusion, Nature 371, 37–43.

    PubMed  CAS  Google Scholar 

  99. Chan, D. C., Fass, D., Berger, J. M., and Kim, P. S. (1997) Core structure of gp41 from the HIV envelope glycoprotein, Cell 89, 263–273.

    PubMed  CAS  Google Scholar 

  100. Stiasny, K., Allison, S. L., Mandl, C. W., and Heinz, F. X. (2001) Role of metastability and acidic pH in membrane fusion by tick-borne encephalitis virus, J Virol 75, 7392–7398.

    PubMed  CAS  Google Scholar 

  101. Orosz, A., Wisniewski, J., and Wu, C. (1996) Regulation of Drosophila heat shock factor trimerization: global sequence requirements and independence of nuclear localization, Mol Cell Biol 16, 7018–7030.

    PubMed  CAS  Google Scholar 

  102. Xiao, T., Gardner, K. H., and Sprang, S. R. (2002) Cosolvent-induced transformation of a death domain tertiary structure, Proc Natl Acad Sci USA 99, 11151–11156.

    PubMed  CAS  Google Scholar 

  103. Kuloglu, E. S., McCaslin, D. R., Markley, J. L., and Volkman, B. F. (2002) Structural rearrangement of human lymphotactin, a C chemokine, under physiological solution conditions, J Biol Chem 277, 17863–17870.

    PubMed  CAS  Google Scholar 

  104. Zubkov, S., Gronenborn, A. M., Byeon, I. J., and Mohanty, S. (2005) Structural consequences of the pH-induced conformational switch in A. polyphemus pheromone-binding protein: mechanisms of ligand release, J Mol Biol 354, 1081–1090.

    PubMed  CAS  Google Scholar 

  105. Joerger, A. C., Rajagopalan, S., Natan, E., Veprintsev, D. B., Robinson, C. V., and Fersht, A. R. (2009) Structural evolution of p53, p63, and p73: implication for heterotetramer formation, Proc Natl Acad Sci USA 106, 17705–17710.

    PubMed  CAS  Google Scholar 

  106. Cordell, S. C., Anderson, R. E., and Lowe, J. (2001) Crystal structure of the bacterial cell division inhibitor MinC, EMBO J 20, 2454–2461.

    PubMed  CAS  Google Scholar 

  107. Xu, Q., and Minor, D. L., Jr. (2009) Crystal structure of a trimeric form of the K(V)7.1 (KCNQ1) A-domain tail coiled-coil reveals structural plasticity and context dependent changes in a putative coiled-coil trimerization motif, Protein Sci 18, 2100–2114.

    PubMed  CAS  Google Scholar 

  108. Schellenberg, M. J., Ritchie, D. B., Wu, T., Markin, C. J., Spyracopoulos, L., and Macmillan, A. M. (2010) Context-Dependent Remodeling of Structure in Two Large Protein Fragments, J Mol Biol 402, 720–730.

    Google Scholar 

  109. Guo, J. T., Jaromczyk, J. W., and Xu, Y. (2007) Analysis of chameleon sequences and their implications in biological processes, Proteins 67, 548–558.

    PubMed  CAS  Google Scholar 

  110. Mezei, M. (1998) Chameleon sequences in the PDB, Protein Eng 11, 411–414.

    PubMed  CAS  Google Scholar 

  111. Tan, S., and Richmond, T. J. (1998) Crystal structure of the yeast MATalpha2/MCM1/DNA ternary complex, Nature 391, 660–666.

    PubMed  CAS  Google Scholar 

  112. Abel, K., Yoder, M. D., Hilgenfeld, R., and Jurnak, F. (1996) An alpha to beta conformational switch in EF-Tu, Structure 4, 1153–1159.

    PubMed  CAS  Google Scholar 

  113. Polekhina, G., Thirup, S., Kjeldgaard, M., Nissen, P., Lippmann, C., and Nyborg, J. (1996) Helix unwinding in the effector region of elongation factor EF-Tu-GDP, Structure 4, 1141–1151.

    PubMed  CAS  Google Scholar 

  114. Chen, Y. W., Allen, M. D., Veprintsev, D. B., Lowe, J., and Bycroft, M. (2004) The structure of the AXH domain of spinocerebellar ataxin-1, J Biol Chem 279, 3758–3765.

    PubMed  CAS  Google Scholar 

  115. de Chiara, C., Menon, R. P., Adinolfi, S., de Boer, J., Ktistaki, E., Kelly, G., Calder, L., Kioussis, D., and Pastore, A. (2005) The AXH domain adopts alternative folds the solution structure of HBP1 AXH, Structure 13, 743–753.

    PubMed  Google Scholar 

  116. Hamada, K., Shimizu, T., Yonemura, S., Tsukita, S., and Hakoshima, T. (2003) Structural basis of adhesion-molecule recognition by ERM proteins revealed by the crystal structure of the radixin-ICAM-2 complex, EMBO J 22, 502–514.

    PubMed  CAS  Google Scholar 

  117. Kitano, K., Yusa, F., and Hakoshima, T. (2006) Structure of dimerized radixin FERM domain suggests a novel masking motif in C-terminal residues 295-304, Acta Crystallogr Sect F Struct Biol Cryst Commun 62, 340–345.

    PubMed  Google Scholar 

  118. Zimmer, J., Li, W., and Rapoport, T. A. (2006) A novel dimer interface and conformational changes revealed by an X-ray structure of B. subtilis SecA, J Mol Biol 364, 259–265.

    PubMed  CAS  Google Scholar 

  119. Tidow, H., Lauber, T., Vitzithum, K., Sommerhoff, C. P., Rosch, P., and Marx, U. C. (2004) The solution structure of a chimeric LEKTI domain reveals a chameleon sequence, Biochemistry 43, 11238–11247.

    PubMed  CAS  Google Scholar 

  120. Ditzel, L., Lowe, J., Stock, D., Stetter, K. O., Huber, H., Huber, R., and Steinbacher, S. (1998) Crystal structure of the thermosome, the archaeal chaperonin and homolog of CCT, Cell 93, 125–138.

    PubMed  CAS  Google Scholar 

  121. Klumpp, M., Baumeister, W., and Essen, L. O. (1997) Structure of the substrate binding domain of the thermosome, an archaeal group II chaperonin, Cell 91, 263–270.

    PubMed  CAS  Google Scholar 

  122. Chothia, C. (1984) Principles that determine the structure of proteins, Annu Rev Biochem 53, 537–572.

    PubMed  CAS  Google Scholar 

  123. Chothia, C., and Finkelstein, A. V. (1990) The classification and origins of protein folding patterns, Annu Rev Biochem 59, 1007–1039.

    PubMed  CAS  Google Scholar 

  124. Sternberg, M. J., and Thornton, J. M. (1976) On the conformation of proteins: the handedness of the beta-strand-alpha-helix-beta-strand unit, J Mol Biol 105, 367–382.

    PubMed  CAS  Google Scholar 

  125. Sternberg, M. J., and Thornton, J. M. (1977) On the conformation of proteins: the handedness of the connection between parallel beta-strands, J Mol Biol 110, 269–283.

    PubMed  CAS  Google Scholar 

  126. Belogurov, G. A., Vassylyeva, M. N., Svetlov, V., Klyuyev, S., Grishin, N. V., Vassylyev, D. G., and Artsimovitch, I. (2007) Structural basis for converting a general transcription factor into an operon-specific virulence regulator, Mol Cell 26, 117–129.

    PubMed  CAS  Google Scholar 

  127. Guzzo, C. R., Nagem, R. A., Barbosa, J. A., and Farah, C. S. (2007) Structure of Xanthomonas axonopodis pv. citri YaeQ reveals a new compact protein fold built around a variation of the PD-(D/E)XK nuclease motif, Proteins 69, 644–651.

    PubMed  CAS  Google Scholar 

  128. Essen, L. O., Perisic, O., Cheung, R., Katan, M., and Williams, R. L. (1996) Crystal structure of a mammalian phosphoinositide-specific phospholipase C delta, Nature 380, 595–602.

    PubMed  CAS  Google Scholar 

  129. Sutton, R. B., Davletov, B. A., Berghuis, A. M., Sudhof, T. C., and Sprang, S. R. (1995) Structure of the first C2 domain of synaptotagmin I: a novel Ca2+/phospholipid-binding fold, Cell 80, 929–938.

    PubMed  CAS  Google Scholar 

  130. Andreeva, A., Howorth, D., Brenner, S. E., Hubbard, T. J., Chothia, C., and Murzin, A. G. (2004) SCOP database in 2004: refinements integrate structure and sequence family data, Nucleic Acids Res 32, D226–229.

    PubMed  CAS  Google Scholar 

  131. Andreeva, A., Howorth, D., Chandonia, J. M., Brenner, S. E., Hubbard, T. J., Chothia, C., and Murzin, A. G. (2008) Data growth and its impact on the SCOP database: new developments, Nucleic Acids Res 36, D419–425.

    PubMed  CAS  Google Scholar 

  132. Cuff, A., Redfern, O. C., Greene, L., Sillitoe, I., Lewis, T., Dibley, M., Reid, A., Pearl, F., Dallman, T., Todd, A., Garratt, R., Thornton, J., and Orengo, C. (2009) The CATH hierarchy revisited-structural divergence in domain superfamilies and the continuity of fold space, Structure 17, 1051–1062.

    PubMed  CAS  Google Scholar 

  133. Hadley, C., and Jones, D. T. (1999) A systematic comparison of protein structure classifications: SCOP, CATH and FSSP, Structure 7, 1099–1112.

    PubMed  CAS  Google Scholar 

  134. Day, R., Beck, D. A., Armen, R. S., and Daggett, V. (2003) A consensus view of fold space: combining SCOP, CATH, and the Dali Domain Dictionary, Protein Sci 12, 2150–2160.

    PubMed  CAS  Google Scholar 

  135. Holm, L., and Park, J. (2000) DaliLite workbench for protein structure comparison, Bioinformatics 16, 566–567.

    PubMed  CAS  Google Scholar 

  136. Suhrer, S. J., Wiederstein, M., Gruber, M., and Sippl, M. J. (2009) COPS – a novel workbench for explorations in fold space, Nucleic Acids Res 37, W539–544.

    PubMed  CAS  Google Scholar 

  137. Li, Z., Ye, Y., and Godzik, A. (2006) Flexible Structural Neighborhood – a database of protein structural similarities and alignments, Nucleic Acids Res 34, D277–280.

    PubMed  CAS  Google Scholar 

  138. Bray, J. E., Todd, A. E., Pearl, F. M., Thornton, J. M., and Orengo, C. A. (2000) The CATH Dictionary of Homologous Superfamilies (DHS): a consensus approach for identifying distant structural homologues, Protein Eng 13, 153–165.

    PubMed  CAS  Google Scholar 

  139. Waterhouse, A. M., Procter, J. B., Martin, D. M., Clamp, M., and Barton, G. J. (2009) Jalview Version 2 – a multiple sequence alignment editor and analysis workbench, Bioinformatics 25, 1189–1191.

    PubMed  CAS  Google Scholar 

  140. Ashkenazy, H., Erez, E., Martz, E., Pupko, T., and Ben-Tal, N. (2010) ConSurf 2010: calculating evolutionary conservation in sequence and structure of proteins and nucleic acids, Nucleic Acids Res 38 Suppl, W529–533.

    PubMed  CAS  Google Scholar 

  141. (2010) The Universal Protein Resource (UniProt) in 2010, Nucleic Acids Res 38, D142–148.

    Google Scholar 

  142. Sayers, E. W., Barrett, T., Benson, D. A., Bryant, S. H., Canese, K., Chetvernin, V., Church, D. M., DiCuccio, M., Edgar, R., Federhen, S., Feolo, M., Geer, L. Y., Helmberg, W., Kapustin, Y., Landsman, D., Lipman, D. J., Madden, T. L., Maglott, D. R., Miller, V., Mizrachi, I., Ostell, J., Pruitt, K. D., Schuler, G. D., Sequeira, E., Sherry, S. T., Shumway, M., Sirotkin, K., Souvorov, A., Starchenko, G., Tatusova, T. A., Wagner, L., Yaschenko, E., and Ye, J. (2009) Database resources of the National Center for Biotechnology Information, Nucleic Acids Res 37, D5–15.

    PubMed  CAS  Google Scholar 

  143. Holm, L., and Rosenstrom, P. (2010) Dali server: conservation mapping in 3D, Nucleic Acids Res 38 Suppl, W545–549.

    PubMed  CAS  Google Scholar 

  144. Pearson, W. R., and Lipman, D. J. (1988) Improved tools for biological sequence comparison, Proc Natl Acad Sci USA 85, 2444–2448.

    PubMed  CAS  Google Scholar 

  145. Gibrat, J. F., Madej, T., and Bryant, S. H. (1996) Surprising similarities in structure comparison, Curr Opin Struct Biol 6, 377–385.

    PubMed  CAS  Google Scholar 

  146. Orengo, C. A., and Taylor, W. R. (1996) SSAP: sequential structure alignment program for protein structure comparison, Methods Enzymol 266, 617–635.

    PubMed  CAS  Google Scholar 

  147. Ye, Y., and Godzik, A. (2003) Flexible structure alignment by chaining aligned fragment pairs allowing twists, Bioinformatics 19 Suppl 2, ii246–255.

    Google Scholar 

  148. Shindyalov, I. N., and Bourne, P. E. (1998) Protein structure alignment by incremental combinatorial extension (CE) of the optimal path, Protein Eng 11, 739–747.

    PubMed  CAS  Google Scholar 

  149. Ortiz, A. R., Strauss, C. E., and Olmea, O. (2002) MAMMOTH (matching molecular models obtained from theory): an automated method for model comparison, Protein Sci 11, 2606–2621.

    PubMed  CAS  Google Scholar 

  150. Sippl, M. J., and Wiederstein, M. (2008) A note on difficult structure alignment problems, Bioinformatics 24, 426–427.

    PubMed  CAS  Google Scholar 

  151. Zhang, Y., and Skolnick, J. (2005) TM-align: a protein structure alignment algorithm based on the TM-score, Nucleic Acids Res 33, 2302–2309.

    PubMed  CAS  Google Scholar 

  152. Jayasinghe, S., Hristova, K., and White, S. H. (2001) MPtopo: A database of membrane protein topology, Protein Sci 10, 455–458.

    PubMed  CAS  Google Scholar 

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  1. MRC Laboratory of Molecular Biology, Cambridge, UK

    Antonina Andreeva

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  1. Antonina Andreeva
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  1. Molsoft L.L.C., Sorrento Valley Road 11199, S209 San Diego, 92121, California, USA

    Andrew J. W. Orry

  2. Skaggs School of Pharmacy &, Pharmaceutical Sciences, University of California, San Diego, Gilman Drive 9500, La Jolla, 92093, California, USA

    Ruben Abagyan

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Andreeva, A. (2011). Classification of Proteins: Available Structural Space for Molecular Modeling. In: Orry, A., Abagyan, R. (eds) Homology Modeling. Methods in Molecular Biology, vol 857. Humana Press. https://doi.org/10.1007/978-1-61779-588-6_1

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  • DOI: https://doi.org/10.1007/978-1-61779-588-6_1

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